B3GALNT2

Chr 1AR

beta-1,3-N-acetylgalactosaminyltransferase 2

Also known as: B3GalNAc-T2, MDDGA11

NCBI Gene: 148789 ENSG00000162885 UniProt: Q8NCR0 OMIM: 610194

The protein is a beta-1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure on N- and O-glycans and is specifically involved in alpha-dystroglycan glycosylation, which is required for binding laminin and other extracellular proteins. Biallelic mutations cause congenital muscular dystrophy-dystroglycanopathy type A11, characterized by congenital onset muscular dystrophy with brain and eye anomalies. This condition follows autosomal recessive inheritance.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.841 OMIM phenotype

Clinical Summary— B3GALNT2

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Gene-Disease Validity (ClinGen)

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

72 unique Pathogenic / Likely Pathogenic· 282 VUS of 704 total submissions

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Clinical Trials

1 active or recruiting trial — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.84LOEUF

pLI 0.000

Z-score 2.20

OE 0.55 (0.36–0.84)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.95Z-score

OE missense 0.84 (0.75–0.93)

222 obs / 265.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.55 (0.36–0.84)

0≤0.351.4

Missense OE?0.84 (0.75–0.93)

0≤0.61.4

Synonymous OE?0.91

0≤1.21.6

LoF obs/exp: 15 / 27.4Missense obs/exp: 222 / 265.6Syn Z: 0.72

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitiveB3GALNT2-related muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type ALOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.6355th %ile

GOF

0.6735th %ile

LOF

0.2678th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

704 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic47

Likely Pathogenic25

VUS282

Likely Benign274

Benign53

Conflicting12

Pathogenic

Likely Pathogenic

282

VUS

274

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	40	0	7	0	47
Likely Pathogenic	19	5	1	0	25
VUS	11	231	37	3	282
Likely Benign	3	4	119	148	274
Benign	0	3	49	1	53
Conflicting	—				12
Total	73	243	213	152	693

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

50 pathogenic / likely-pathogenic (of 67) ClinVar copy-number / structural variants overlap B3GALNT2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →